This run was generated using rMAP version 1.0 performed on 2020-09-03… Thank you for using this pipeline!!


Assembly summary statistics


Field Description
SampleID Name of the sample
TrimReads Total number of reads after quality filtering
MeanReadLen Average read length after quality filtering
Contigs Number of contigs of the draft genome (>200bp)
GenomeLength Length (bp) of the draft genome
LargestContig Length (bp) of the largest contig in the genome
N50 Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content GC content (%) of the draft genome
Depth Number of times each nucleotide position in the draft genome has a read that aligns to that position


SampleID TrimReads MeanReadLen Contigs GenomeLength LargestContig N50 GC-Content Depth
SRR8948878 1595020 149 68 3101402 545479 273671 37.21 76X
SRR8948879 1588168 149 79 3010836 603711 179463 37.44 78X
SRR8948880 1594518 149 102 3166205 417860 239597 37.18 75X
SRR8948881 1591214 149 44 2924312 516731 202453 37.46 81X
SRR8948882 1586702 149 170 2925331 107207 46219 37.69 80X
SRR8948883 1579276 149 180 2964061 113751 44888 37.74 79X
SRR8948884 1591394 149 57 2934130 644112 179342 37.47 80X
SRR8948885 1584504 149 59 3363692 424585 243114 40.43 70X
SRR8948886 1584116 149 56 2786637 344853 172313 38.08 84X
SRR8948887 1585296 149 89 2984341 603711 185199 37.49 79X
SRR8948888 1576542 149 57 3024061 544043 207386 37.28 77X
SRR8948889 1590020 149 290 5897762 544519 66637 37.49 40X
SRR8948890 1588164 149 52 3016695 544186 207384 37.27 78X
SRR8948891 1589798 149 69 3037920 544195 219893 37.30 77X

Select the parameter

Number of reads
## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

Average number of reads per sample = 1587481

Average read length

Average read length per sample = 149 bp

Number of contigs

Average number of contigs per sample = 98

Genome length

Average genome length per sample = 3224099 bp

Largest contig length

Average largest contig length per sample = 464210 bp

N50

Average N50 per sample = 176254 bp

GC content

Average GC content per sample = 37.681%

Sequencing depth

Average sequencing depth = 75.286X

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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Antimicrobial Resistance Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product
Resistance Antibiotic that the gene confers resistance to


Select the samples and the database

SRR8948878
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00007 82257 82754 dfrG_1 0/0 100 100.0 AB205645 dfrG Trimethoprim
contig00027 2694 3456 erm(B)_18 1/1 100 99.1 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 172990 174486 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 31907 33826 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 78017 78511 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00007 82257 82754 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00008 24880 26607 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00008 23268 24321 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 519193 520347 emeA 1/27 97.7 97.1 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00027 2719 3464 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00004 172990 174486 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 31907 33826 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2719 3456 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00006 213113 213946 (MLS)mph(D) 0/0 100 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 31907 33826 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 78017 78511 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00007 82257 82754 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2719 3456 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00006 213113 213946 (MLS)mph(D) 0/0 100 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 31907 33826 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 78017 78511 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00007 82257 82754 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 78017 78511 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00007 82257 82754 DFRG 0/0 100.0 100.0 MEG_2579 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRG NA
contig00008 24966 26400 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00008 23268 24321 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00027 2694 3456 ERMB 1/1 100.0 99.1 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00004 172990 174486 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00002 31907 33826 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
SRR8948879
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 3187 3834 cat(pC221)_1 0/0 100 97.7 X02529 cat(pC221) Chloramphenicol
contig00011 56585 58081 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00007 124979 126898 tet(M)_13 0/0 100 99.9 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
contig00033 2093 4699 VanHAX_2 0/0 100 100.0 M97297 VanHAX Vancomycin, Teicoplanin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00013 25119 26846 efrA 0/0 100.0 99.3 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00013 23507 24560 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00006 173315 174469 emeA 1/27 97.7 97.0 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00028 3187 3834 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00011 56585 58081 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00007 124979 126898 tetM 0/0 100.0 99.9 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00045 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00033 3054 4085 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00033 2093 3061 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00033 51 746 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00033 724 1878 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00033 4091 4699 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00028 9615 10100 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00033 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00033 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00033 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00033 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00033 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00028 9615 10100 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00011 56585 58081 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00028 3187 3834 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00007 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00045 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00033 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00033 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00033 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00033 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00033 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00028 9615 10100 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00011 56585 58081 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00028 3187 3834 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00007 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00045 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 3187 3834 CATA 0/0 100.0 100.0 MEG_1591 Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA NA
contig00001 182045 182539 DFRE 0/0 100.0 97.6 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00013 25205 26639 EFRA 1/1 98.5 99.1 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00013 23507 24560 EFRB 6/6 96.7 97.6 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00011 56585 58081 LSA 0/0 100.0 99.4 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00007 124979 126898 TETM 0/0 100.0 99.9 MEG_7145 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
contig00045 728 1045 TETU 0/0 100.0 99.4 MEG_7204 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_regulator:TETU NA
contig00033 2093 4699 VANHA 0/0 100.0 100.0 MEG_7410 Drugs:Glycopeptides:VanA-type_resistance_protein:VANHA NA
contig00028 9615 10100 VANRA 0/0 100.0 100.0 MEG_7452 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00033 51 746 VANRA 0/0 100.0 100.0 MEG_7453 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00033 724 1878 VANRA 0/0 100.0 100.0 MEG_7454 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
SRR8948880
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 ant(6)-Ia_1 0/0 96.9 100.0 AF330699 ant(6)-Ia Streptomycin
contig00039 1557 2204 cat(pC221)_1 0/0 100.0 97.7 X02529 cat(pC221) Chloramphenicol
contig00008 82257 82754 dfrG_1 0/0 100.0 100.0 AB205645 dfrG Trimethoprim
contig00031 2694 3456 erm(B)_18 1/1 100.0 99.1 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 172990 174486 lsa(A)_1 0/0 100.0 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 32394 34313 tet(M)_10 0/0 100.0 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
contig00040 1 2426 VanHAX_2 0/0 93.1 100.0 M97297 VanHAX Vancomycin, Teicoplanin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 51 881 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00009 78017 78511 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00008 82257 82754 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00003 24880 26607 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00003 23268 24321 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 25016 26170 emeA 1/27 97.7 97.1 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00039 1557 2204 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00031 2719 3464 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00004 172990 174486 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 32394 34313 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00046 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00040 781 1812 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00040 1818 2426 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00056 380 1291 vanYA 0/0 100.0 100.0 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 (AGly)ant6-Ia 0/0 96.9 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00040 781 1812 (Gly)vanA-A 0/0 100.0 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00040 1818 2426 (Gly)vanX-A 0/0 100.0 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00056 380 1291 (Gly)vanY-A 0/0 100.0 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00031 2719 3456 (MLS)erm(B) 0/0 100.0 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100.0 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00005 213113 213946 (MLS)mph(D) 0/0 100.0 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00039 1557 2204 (Phe)cat-pC221 0/0 100.0 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00002 32394 34313 (Tet)tetM 0/0 100.0 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00046 728 1045 (Tet)tetU 0/0 100.0 99.4 U01917:413-730 (Tet)tetU NA
contig00009 78017 78511 (Tmt)dfrE 0/0 100.0 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00008 82257 82754 (Tmt)dfrG 0/0 100.0 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 (AGly)ant6-Ia 0/0 96.9 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00040 781 1812 (Gly)vanA-A 0/0 100.0 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00040 1818 2426 (Gly)vanX-A 0/0 100.0 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00056 380 1291 (Gly)vanY-A 0/0 100.0 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00031 2719 3456 (MLS)erm(B) 0/0 100.0 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100.0 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00005 213113 213946 (MLS)mph(D) 0/0 100.0 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00039 1557 2204 (Phe)cat-pC221 0/0 100.0 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00002 32394 34313 (Tet)tetM 0/0 100.0 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00046 728 1045 (Tet)tetU 0/0 100.0 99.4 U01917:413-730 (Tet)tetU NA
contig00009 78017 78511 (Tmt)dfrE 0/0 100.0 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00008 82257 82754 (Tmt)dfrG 0/0 100.0 100.0 AB205645:1013-1510 (Tmt)dfrG NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 ANT6 0/0 96.9 100.0 MEG_994 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT6 NA
contig00039 1557 2204 CATA 0/0 100.0 100.0 MEG_1591 Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA NA
contig00009 78017 78511 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00008 82257 82754 DFRG 0/0 100.0 100.0 MEG_2579 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRG NA
contig00003 24966 26400 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00003 23268 24321 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00031 2694 3456 ERMB 1/1 100.0 99.1 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00004 172990 174486 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00002 32394 34313 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
contig00046 728 1045 TETU 0/0 100.0 99.4 MEG_7204 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_regulator:TETU NA
contig00040 1 2426 VANHA 0/0 93.1 100.0 MEG_7410 Drugs:Glycopeptides:VanA-type_resistance_protein:VANHA NA
contig00056 380 1291 VANRA 0/0 100.0 100.0 MEG_7458 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
SRR8948881
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 56301 57797 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00029 524 2464 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 72187 72681 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00007 141691 143418 efrA 0/0 100.0 99.2 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00007 143977 145030 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00006 170401 171555 emeA 1/27 97.7 96.9 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00010 56301 57797 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00029 524 2449 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 56301 57797 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00029 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00001 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 56301 57797 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00029 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00001 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 72187 72681 DFRE 0/0 100.0 97.6 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00007 141898 143332 EFRA 1/1 98.5 99.0 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00007 143977 145030 EFRB 6/6 96.7 97.6 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00010 56301 57797 LSA 0/0 100.0 99.4 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00029 524 2464 TETS 0/0 100.0 99.9 MEG_7200 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETS NA
SRR8948882
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 aac(6’)-aph(2’’)_1 0/0 93.3 99.9 M13771 aac(6’)-aph(2’’) Amikacin, Gentamicin, Tobramycin
contig00010 31434 31982 aac(6’)-Ii_1 0/0 100.0 99.6 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00064 6660 7568 ant(6)-Ia_1 0/0 100.0 100.0 AF330699 ant(6)-Ia Streptomycin
contig00064 8200 8994 aph(3’)-III_1 0/0 100.0 100.0 M26832 aph(3’)-III Amikacin
contig00064 12761 13523 erm(B)_18 1/1 100.0 99.5 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 80444 81922 msr(C)_1 0/0 100.0 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00073 4890 7496 VanHAX_2 0/0 100.0 99.9 M97297 VanHAX Vancomycin, Teicoplanin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 AAC(6’)-Ie-APH(2’’)-Ia 0/0 93.3 99.9 GU565967.1:26419-24979 AAC(6’)-Ie-APH(2’’)-Ia is an aminoglycoside acetyltransferase encoded by plasmids and transposons in S. aureus E. faecalis E. faecium and Staphylococcus warneri aminoglycoside
contig00010 31434 31982 AAC(6’)-Ii 0/0 100.0 99.6 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00064 6738 7568 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00064 8200 8994 APH(3’)-IIIa 0/0 100.0 100.0 CP004067:52914-53709 APH(3’)-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp. aminoglycoside
contig00008 39083 40369 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00064 12753 13498 ErmB 1/1 99.9 99.2 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00004 80444 81922 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00064 7565 8107 SAT-4 0/0 100.0 99.8 U01945:373-916 SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE/G4 plasmid gene sequence by Jacob et al 1994. nucleoside
contig00073 5504 6535 vanA 0/0 100.0 99.9 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00073 6528 7496 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00073 8843 9538 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00073 7711 8865 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00073 4890 5498 vanXA 0/0 100.0 99.8 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00073 3551 4462 vanYA 0/0 100.0 99.8 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00073 2913 3398 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 (AGly)aac6-Aph2 0/0 93.3 99.9 M13771:304-1743 (AGly)aac6-Aph2 NA
contig00010 31434 31982 (AGly)aac6-Ii 0/0 100.0 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00064 6660 7568 (AGly)ant6-Ia 0/0 100.0 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00064 8200 8994 (AGly)aph(3’’)-III 0/0 100.0 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00064 7565 8107 (AGly)sat4A 0/0 100.0 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00073 5504 6535 (Gly)vanA-A 0/0 100.0 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00073 6528 7496 (Gly)vanH-A 0/0 100.0 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00073 8843 9538 (Gly)vanR-A 0/0 100.0 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00073 7711 8865 (Gly)vanS-A 0/0 100.0 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00073 4890 5498 (Gly)vanX-A 0/0 100.0 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00073 3551 4462 (Gly)vanY-A 0/0 100.0 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00073 2913 3398 (Gly)vanZ-A 0/0 100.0 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00064 12761 13498 (MLS)erm(B) 0/0 100.0 99.9 M11180:714-1451 (MLS)erm(B) NA
contig00004 80444 81922 (MLS)msr(C) 0/0 100.0 98.9 AY004350:496-1974 (MLS)msr(C) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 (AGly)aac6-Aph2 0/0 93.3 99.9 M13771:304-1743 (AGly)aac6-Aph2 NA
contig00010 31434 31982 (AGly)aac6-Ii 0/0 100.0 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00064 6660 7568 (AGly)ant6-Ia 0/0 100.0 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00064 8200 8994 (AGly)aph(3’’)-III 0/0 100.0 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00064 7565 8107 (AGly)sat4A 0/0 100.0 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00073 5504 6535 (Gly)vanA-A 0/0 100.0 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00073 6528 7496 (Gly)vanH-A 0/0 100.0 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00073 8843 9538 (Gly)vanR-A 0/0 100.0 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00073 7711 8865 (Gly)vanS-A 0/0 100.0 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00073 4890 5498 (Gly)vanX-A 0/0 100.0 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00073 3551 4462 (Gly)vanY-A 0/0 100.0 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00073 2913 3398 (Gly)vanZ-A 0/0 100.0 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00064 12761 13498 (MLS)erm(B) 0/0 100.0 99.9 M11180:714-1451 (MLS)erm(B) NA
contig00004 80444 81922 (MLS)msr(C) 0/0 100.0 98.9 AY004350:496-1974 (MLS)msr(C) NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 31434 31982 AAC6-PRIME 0/0 100.0 100.0 MEG_84 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC6-PRIME NA
contig00126 374 1719 AAC6-PRIME 0/0 93.2 99.9 MEG_364 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC6-PRIME NA
contig00064 6660 7568 ANT6 0/0 100.0 100.0 MEG_994 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT6 NA
contig00064 8200 8994 APH2-DPRIME 0/0 100.0 100.0 MEG_1016 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH2-DPRIME NA
contig00008 39083 40369 EFMA 0/0 100.0 100.0 MEG_2704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EFMA NA
contig00064 12761 13523 ERMB 1/1 100.0 99.5 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00004 80444 81922 MSRC 0/0 100.0 98.9 MEG_4071 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRC NA
contig00064 7565 8107 SAT 0/0 100.0 100.0 MEG_6166 Drugs:Nucleosides:Streptothricin_acetyltransferase:SAT NA
contig00073 4890 7496 VANHA 0/0 100.0 99.9 MEG_7410 Drugs:Glycopeptides:VanA-type_resistance_protein:VANHA NA
contig00073 2913 3398 VANRA 0/0 100.0 100.0 MEG_7452 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00073 3551 4462 VANRA 0/0 100.0 99.8 MEG_7458 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00073 7711 8865 VANRA 0/0 100.0 100.0 MEG_7454 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00073 8843 9538 VANRA 0/0 100.0 100.0 MEG_7453 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
SRR8948883
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 aac(6’)-Ii_1 0/0 100 98.9 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00108 2185 3093 ant(6)-Ia_1 0/0 100 100.0 AF330699 ant(6)-Ia Streptomycin
contig00080 4495 5142 cat(pC221)_1 0/0 100 97.7 X02529 cat(pC221) Chloramphenicol
contig00137 136 898 erm(B)_18 1/1 100 99.0 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 56772 58250 msr(C)_1 0/0 100 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00021 22046 23965 tet(M)_13 0/0 100 100.0 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
contig00097 2093 4699 VanHAX_2 0/0 100 100.0 M97297 VanHAX Vancomycin, Teicoplanin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 AAC(6’)-Ii 0/0 100.0 98.9 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00108 2263 3093 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00070 4109 4604 dfrF 1/1 100.0 99.6 AF028812:392-887 dfrF is a chromosome-encoded dihydrofolate reductase found in Streptococcus pyogenes diaminopyrimidine
contig00006 37430 38716 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00080 4495 5142 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00137 161 906 ErmB 1/1 99.9 99.6 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00003 56772 58250 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00021 22046 23965 tetM 0/0 100.0 100.0 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00123 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00097 3054 4085 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00097 2093 3061 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00097 51 746 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00097 724 1878 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00097 4091 4699 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00112 1930 2841 vanYA 0/0 100.0 100.0 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00112 1292 1777 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 (AGly)aac6-Ii 0/0 100 98.9 L12710:169-717 (AGly)aac6-Ii NA
contig00108 2185 3093 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00097 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00097 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00097 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00097 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00097 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00112 1930 2841 (Gly)vanY-A 0/0 100 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00112 1292 1777 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00137 161 898 (MLS)erm(B) 0/0 100 99.5 M11180:714-1451 (MLS)erm(B) NA
contig00003 56772 58250 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00080 4495 5142 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00021 22046 23965 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00123 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00070 4109 4604 (Tmt)dfrF 1/1 100 99.6 NG_047755:101-595 (Tmt)dfrF NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 (AGly)aac6-Ii 0/0 100 98.9 L12710:169-717 (AGly)aac6-Ii NA
contig00108 2185 3093 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00097 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00097 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00097 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00097 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00097 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00112 1930 2841 (Gly)vanY-A 0/0 100 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00112 1292 1777 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00137 161 898 (MLS)erm(B) 0/0 100 99.5 M11180:714-1451 (MLS)erm(B) NA
contig00003 56772 58250 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00080 4495 5142 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00021 22046 23965 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00123 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00070 4109 4604 (Tmt)dfrF 1/1 100 99.6 NG_047755:101-595 (Tmt)dfrF NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 AAC6-PRIME 0/0 100 99.6 MEG_139 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC6-PRIME NA
contig00108 2185 3093 ANT6 0/0 100 100.0 MEG_994 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT6 NA
contig00080 4495 5142 CATA 0/0 100 100.0 MEG_1591 Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA NA
contig00070 4109 4604 DFRF 1/1 100 99.6 MEG_2578 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRF NA
contig00006 37430 38716 EFMA 0/0 100 100.0 MEG_2704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EFMA NA
contig00137 136 898 ERMB 1/1 100 99.0 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00003 56772 58250 MSRC 0/0 100 98.9 MEG_4071 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRC NA
contig00021 22046 23965 TETM 0/0 100 100.0 MEG_7145 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
contig00123 728 1045 TETU 0/0 100 99.4 MEG_7204 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_regulator:TETU NA
contig00097 2093 4699 VANHA 0/0 100 100.0 MEG_7410 Drugs:Glycopeptides:VanA-type_resistance_protein:VANHA NA
contig00097 51 746 VANRA 0/0 100 100.0 MEG_7453 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00097 724 1878 VANRA 0/0 100 100.0 MEG_7454 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00112 1292 1777 VANRA 0/0 100 100.0 MEG_7452 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00112 1930 2841 VANRA 0/0 100 100.0 MEG_7458 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
SRR8948884
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 57049 58545 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00031 524 2464 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00002 72187 72681 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00013 35717 37444 efrA 0/0 100.0 99.2 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00013 38003 39056 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00004 173480 174634 emeA 1/27 97.7 96.9 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00008 57049 58545 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00031 524 2449 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 57049 58545 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00002 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00031 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00002 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 57049 58545 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00002 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00031 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00002 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00002 72187 72681 DFRE 0/0 100.0 97.6 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00013 35924 37358 EFRA 1/1 98.5 99.0 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00013 38003 39056 EFRB 6/6 96.7 97.6 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00008 57049 58545 LSA 0/0 100.0 99.4 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00031 524 2464 TETS 0/0 100.0 99.9 MEG_7200 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETS NA
SRR8948885
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 36401 36898 dfrG_1 0/0 100 100.0 AB205645 dfrG Trimethoprim
contig00018 43312 44074 erm(B)_18 1/1 100 99.6 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00029 796 2736 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
contig00012 20441 22041 VanC1XY_1 0/0 100 99.9 AF162694 VanC1XY Vancomycin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 36401 36898 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00018 43304 44049 ErmB 1/1 99.9 99.1 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00029 796 2721 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
contig00012 21010 22041 vanC 0/0 100.0 99.8 AF162694:1410-2442 VanC is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Ser an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is specific to Enterococcus gallinarum and E. casseliflavus providing intrinsic resistance. glycopeptide
contig00012 17564 18259 vanRC 0/0 100.0 100.0 AF162694:5192-5888 vanRC is a vanR variant found in the vanC gene cluster glycopeptide
contig00012 16489 17574 vanSC 0/0 100.0 99.9 AF162694:5877-6963 vanSC is a vanS variant found in the vanC gene cluster glycopeptide
contig00012 18348 20444 vanTC 0/0 100.0 99.9 AF162694:3007-5104 vanTC is a vanT variant found in the vanC gene cluster glycopeptide
contig00012 20441 21013 vanXYC 0/0 100.0 100.0 AF162694:2438-3011 vanXYC is a vanXY variant found in the vanC gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00012 21010 22041 (Gly)vanC 0/0 100 99.8 AF162694:1411-2442 (Gly)vanC NA
contig00012 17564 18259 (Gly)vanR-C 0/0 100 100.0 AF162694:5193-5888 (Gly)vanR-C NA
contig00012 16489 17574 (Gly)vanS-C 0/0 100 99.4 DQ022190:4672-5757 (Gly)vanS-C NA
contig00012 18348 20444 (Gly)vanT 0/0 100 99.9 AF162694:3008-5104 (Gly)vanT NA
contig00012 20441 21013 (Gly)vanX-Yc 0/0 100 100.0 DQ022190:1233-1805 (Gly)vanX-Yc NA
contig00018 43312 44049 (MLS)erm(B) 0/0 100 100.0 M11180:714-1451 (MLS)erm(B) NA
contig00029 796 2721 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00018 36401 36898 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00012 21010 22041 (Gly)vanC 0/0 100 99.8 AF162694:1411-2442 (Gly)vanC NA
contig00012 17564 18259 (Gly)vanR-C 0/0 100 100.0 AF162694:5193-5888 (Gly)vanR-C NA
contig00012 16489 17574 (Gly)vanS-C 0/0 100 99.4 DQ022190:4672-5757 (Gly)vanS-C NA
contig00012 18348 20444 (Gly)vanT 0/0 100 99.9 AF162694:3008-5104 (Gly)vanT NA
contig00012 20441 21013 (Gly)vanX-Yc 0/0 100 100.0 DQ022190:1233-1805 (Gly)vanX-Yc NA
contig00018 43312 44049 (MLS)erm(B) 0/0 100 100.0 M11180:714-1451 (MLS)erm(B) NA
contig00029 796 2721 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00018 36401 36898 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 36401 36898 DFRG 0/0 100 100.0 MEG_2579 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRG NA
contig00018 43312 44074 ERMB 1/1 100 99.6 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00029 796 2736 TETS 0/0 100 99.9 MEG_7200 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETS NA
contig00012 20441 22041 VANC 0/0 100 99.9 MEG_7373 Drugs:Glycopeptides:VanC-type_resistance_protein:VANC NA
contig00012 16489 17574 VANSC 0/0 100 99.9 MEG_7502 Drugs:Glycopeptides:VanC-type_regulator:VANSC NA
contig00012 17564 18259 VANXYC 0/0 100 100.0 MEG_7584 Drugs:Glycopeptides:VanC-type_resistance_protein:VANXYC NA
contig00012 18348 20444 VANXYC 0/0 100 99.9 MEG_7583 Drugs:Glycopeptides:VanC-type_resistance_protein:VANXYC NA
SRR8948886
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 aac(6’)-Ii_1 0/0 100 98.5 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00019 42610 44088 msr(C)_2 0/0 100 99.5 AF313494 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 AAC(6’)-Ii 0/0 100 98.5 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00019 42610 44088 msrC 0/0 100 99.5 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 (AGly)aac6-Ii 0/0 100 98.5 L12710:169-717 (AGly)aac6-Ii NA
contig00019 42610 44088 (MLS)msr(C) 0/0 100 95.3 AY004350:496-1974 (MLS)msr(C) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 (AGly)aac6-Ii 0/0 100 98.5 L12710:169-717 (AGly)aac6-Ii NA
contig00019 42610 44088 (MLS)msr(C) 0/0 100 95.3 AY004350:496-1974 (MLS)msr(C) NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 AAC6-PRIME 0/0 100 100.0 MEG_139 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC6-PRIME NA
contig00019 42610 44088 MSRC 0/0 100 99.5 MEG_4072 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRC NA
SRR8948887
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 103653 105149 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00006 124979 126898 tet(M)_13 0/0 100 99.9 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00012 25123 26850 efrA 0/0 100.0 99.3 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00012 23511 24564 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00005 173315 174469 emeA 1/27 97.7 97.0 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00008 103653 105149 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00006 124979 126898 tetM 0/0 100.0 99.9 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 103653 105149 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00006 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 103653 105149 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00006 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 DFRE 0/0 100.0 97.6 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00012 25209 26643 EFRA 1/1 98.5 99.1 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00012 23511 24564 EFRB 6/6 96.7 97.6 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00008 103653 105149 LSA 0/0 100.0 99.4 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00006 124979 126898 TETM 0/0 100.0 99.9 MEG_7145 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
SRR8948888
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100902 102398 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 94583 96502 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00015 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00015 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00027 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00003 100902 102398 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 94583 96502 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100902 102398 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94583 96502 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100902 102398 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94583 96502 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00015 7887 9321 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00015 9966 11019 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00027 2516 3278 ERMB 1/1 100.0 99.2 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00003 100902 102398 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00002 94583 96502 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
SRR8948889
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00021 31437 31985 aac(6’)-Ii_1 0/0 100 99.6 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00107 6381 7289 ant(6)-Ia_1 0/0 100 100.0 AF330699 ant(6)-Ia Streptomycin
contig00107 7921 8715 aph(3’)-III_1 0/0 100 100.0 M26832 aph(3’)-III Amikacin
contig00002 100972 102468 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00012 80444 81922 msr(C)_1 0/0 100 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00005 147681 149600 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
contig00115 4892 7498 VanHAX_2 0/0 100 99.9 M97297 VanHAX Vancomycin, Teicoplanin
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00021 31437 31985 AAC(6’)-Ii 0/0 100.0 99.6 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00107 6459 7289 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00107 7921 8715 APH(3’)-IIIa 0/0 100.0 100.0 CP004067:52914-53709 APH(3’)-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp. aminoglycoside
contig00001 77924 78418 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00017 38939 40225 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00044 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00044 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 519114 520268 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00002 100972 102468 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00012 80444 81922 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00107 7286 7828 SAT-4 0/0 100.0 99.8 U01945:373-916 SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE/G4 plasmid gene sequence by Jacob et al 1994. nucleoside
contig00005 147681 149600 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00115 5506 6537 vanA 0/0 100.0 99.9 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00115 6530 7498 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00115 8845 9540 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00115 7713 8867 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00115 4892 5500 vanXA 0/0 100.0 99.8 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00115 3553 4464 vanYA 0/0 100.0 99.8 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00115 2915 3400 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00021 31437 31985 (AGly)aac6-Ii 0/0 100 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00107 6381 7289 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00107 7921 8715 (AGly)aph(3’’)-III 0/0 100 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00107 7286 7828 (AGly)sat4A 0/0 100 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00115 5506 6537 (Gly)vanA-A 0/0 100 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00115 6530 7498 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00115 8845 9540 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00115 7713 8867 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00115 4892 5500 (Gly)vanX-A 0/0 100 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00115 3553 4464 (Gly)vanY-A 0/0 100 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00115 2915 3400 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00002 100972 102468 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00012 80444 81922 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00005 147681 149600 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77924 78418 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00021 31437 31985 (AGly)aac6-Ii 0/0 100 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00107 6381 7289 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00107 7921 8715 (AGly)aph(3’’)-III 0/0 100 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00107 7286 7828 (AGly)sat4A 0/0 100 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00115 5506 6537 (Gly)vanA-A 0/0 100 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00115 6530 7498 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00115 8845 9540 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00115 7713 8867 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00115 4892 5500 (Gly)vanX-A 0/0 100 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00115 3553 4464 (Gly)vanY-A 0/0 100 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00115 2915 3400 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00002 100972 102468 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00012 80444 81922 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00005 147681 149600 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77924 78418 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00021 31437 31985 AAC6-PRIME 0/0 100.0 100.0 MEG_84 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC6-PRIME NA
contig00107 6381 7289 ANT6 0/0 100.0 100.0 MEG_994 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT6 NA
contig00107 7921 8715 APH2-DPRIME 0/0 100.0 100.0 MEG_1016 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH2-DPRIME NA
contig00001 77924 78418 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00017 38939 40225 EFMA 0/0 100.0 100.0 MEG_2704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EFMA NA
contig00044 7887 9321 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00044 9966 11019 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00002 100972 102468 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00012 80444 81922 MSRC 0/0 100.0 98.9 MEG_4071 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRC NA
contig00107 7286 7828 SAT 0/0 100.0 100.0 MEG_6166 Drugs:Nucleosides:Streptothricin_acetyltransferase:SAT NA
contig00005 147681 149600 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
contig00115 4892 7498 VANHA 0/0 100.0 99.9 MEG_7410 Drugs:Glycopeptides:VanA-type_resistance_protein:VANHA NA
contig00115 2915 3400 VANRA 0/0 100.0 100.0 MEG_7452 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00115 3553 4464 VANRA 0/0 100.0 99.8 MEG_7458 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00115 7713 8867 VANRA 0/0 100.0 100.0 MEG_7454 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
contig00115 8845 9540 VANRA 0/0 100.0 100.0 MEG_7453 Drugs:Glycopeptides:VanA-type_regulator:VANRA NA
SRR8948890
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100982 102478 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 94435 96354 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00017 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00017 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00028 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00003 100982 102478 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 94435 96354 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100982 102478 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94435 96354 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100982 102478 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94435 96354 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00017 7887 9321 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00017 9966 11019 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00028 2516 3278 ERMB 1/1 100.0 99.2 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00003 100982 102478 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00002 94435 96354 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA
SRR8948891
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100981 102477 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 92923 94842 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00015 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00015 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00025 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB. lincosamide, macrolide, streptogramin
contig00003 100981 102477 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 92923 94842 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100981 102477 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 92923 94842 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100981 102477 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 92923 94842 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 DFRE 0/0 100.0 97.4 MEG_2577 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRE NA
contig00015 7887 9321 EFRA 1/1 98.5 98.8 MEG_2706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRA NA
contig00015 9966 11019 EFRB 6/6 96.7 97.5 MEG_2707 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:EFRB NA
contig00025 2516 3278 ERMB 1/1 100.0 99.2 MEG_2801 Drugs:MLS:23S_rRNA_methyltransferases:ERMB NA
contig00003 100981 102477 LSA 0/0 100.0 98.9 MEG_3644 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:LSA NA
contig00002 92923 94842 TETM 0/0 100.0 100.0 MEG_7144 Drugs:Tetracyclines:Tetracycline_resistance_ribosomal_protection_proteins:TETM NA


Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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Resfinder
CARD
ARG-ANNOT
NCBI
MEGARES


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Plasmid Profiling

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SRR8948878
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00026 2151 3161 rep9a_1_repA(pAD1) 0/0 100 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00022 10809 11816 rep9b_3_repA(pMG2200) 0/0 100 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00013 55553 56554 rep9c_2_prgW(pCF10) 0/0 100 96.5 AY855841 rep9c_2_prgW(pCF10)_AY855841
contig00002 42100 43305 repUS43_1_CDS12738(DOp1) 0/0 100 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948879
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00028 6614 8104 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00031 5273 6129 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00045 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00029 6028 7521 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00028 2119 3057 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00019 6111 7121 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00007 115500 116705 repUS43_1_CDS12738(DOp1) 0/0 100.0 99.9 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948880
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00033 1494 2984 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00029 5117 6061 rep11a_1_repA(pB82) 0/0 100.0 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00046 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00039 489 1427 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00030 2151 3161 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00025 10809 11816 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00014 55553 56554 rep9c_2_prgW(pCF10) 0/0 100.0 96.5 AY855841 rep9c_2_prgW(pCF10)_AY855841
contig00032 1447 2487 repUS15_2_repA(pNB2354p1) 0/0 100.0 99.8 CP004064 repUS15_2_repA(pNB2354p1)_CP004064
contig00002 42587 43792 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948881
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00028 3326 4048 rep6_1_repA(pS86) 0/0 100 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00018 10842 11825 rep8b_1_repA(pEJ97p1) 0/0 100 99.9 AJ49170 rep8b_1_repA(pEJ97p1)_AJ49170
SRR8948882
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00089 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100 AB178871 rep11a_1_repA(pB82)_AB178871
contig00106 2848 3798 rep14b_3_rep(pRI1) 0/0 100.0 100 EU327398 rep14b_3_rep(pRI1)_EU327398
contig00070 4699 5739 rep17_1_CDS29(pRUM) 0/0 100.0 100 AF507977 rep17_1_CDS29(pRUM)_AF507977
contig00068 8676 10169 rep2_1_orf1(pRE25) 0/0 100.0 100 X92945 rep2_1_orf1(pRE25)_X92945
contig00084 4585 5322 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085 0/0 100.0 100 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085
contig00083 2016 3056 repUS15_1_repA(DO3) 0/0 100.0 100 CP003586 repUS15_1_repA(DO3)_CP003586
SRR8948883
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00080 225 1715 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00088 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00123 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00075 6028 7521 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00080 5272 6210 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00095 2092 3132 repUS15_2_repA(pNB2354p1) 0/0 100.0 99.8 CP004064 repUS15_2_repA(pNB2354p1)_CP004064
SRR8948884
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00030 3326 4048 rep6_1_repA(pS86) 0/0 100 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00019 10842 11825 rep8b_1_repA(pEJ97p1) 0/0 100 99.9 AJ49170 rep8b_1_repA(pEJ97p1)_AJ49170
SRR8948885
## [1] "NO PLASMID FOUND!!"
SRR8948886
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00033 5332 6188 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00038 1065 2105 repUS15_1_repA(DO3) 0/0 100.0 99.9 CP003586 repUS15_1_repA(DO3)_CP003586
SRR8948887
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00027 5332 6188 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00017 6111 7121 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00006 115500 116705 repUS43_1_CDS12738(DOp1) 0/0 100.0 99.9 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948888
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00030 3327 4049 rep6_1_repA(pS86) 0/0 100.0 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 18857 19861 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 104776 105981 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948889
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00141 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00163 2848 3798 rep14b_3_rep(pRI1) 0/0 100.0 100.0 EU327398 rep14b_3_rep(pRI1)_EU327398
contig00110 4699 5739 rep17_1_CDS29(pRUM) 0/0 100.0 100.0 AF507977 rep17_1_CDS29(pRUM)_AF507977
contig00108 8676 10169 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00136 4585 5322 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085 0/0 100.0 100.0 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085
contig00151 4237 4959 rep6_1_repA(pS86) 0/0 100.0 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00018 14859 15866 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00047 12667 13671 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00134 2016 3056 repUS15_1_repA(DO3) 0/0 100.0 100.0 CP003586 repUS15_1_repA(DO3)_CP003586
contig00005 138202 139407 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948890
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 19925 20929 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 104628 105833 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948891
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 19026 20030 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 103116 104321 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584


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Virulence Factor Determination

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SRR8948878
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00002 60574 61584 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00003 383485 384300 cpsA 0/0 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 382688 383488 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 381046 382215 cpsC 0/0 100.0 99.4 NP_816139 (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 379561 381027 cpsD 0/0 100.0 98.8 NP_816138 (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 376981 379491 cpsE 0/0 100.0 99.2 NP_816137 (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 376106 376957 cpsF 0/0 100.0 99.9 NP_816136 (cpsF) CpsF protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 373626 376079 cpsG 0/0 100.0 99.4 NP_816135 (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 373210 373608 cpsH 0/0 100.0 99.8 NP_816134 (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 372012 373151 cpsI 0/0 100.0 100.0 NP_816133 (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 370643 371986 cpsJ 0/0 100.0 100.0 NP_816132 (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 369831 370643 cpsK 0/0 100.0 99.0 NP_816131 (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00017 5642 6880 cylA 0/0 100.0 99.4 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 6877 9021 cylB 0/0 100.0 99.7 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 4658 5641 cylI 0/0 100.0 97.2 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12300 12506 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 9033 12014 cylM 0/0 100.0 99.6 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12625 12909 cylR1 0/0 100.0 98.6 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12910 13110 cylR2 0/0 100.0 99.5 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12075 12266 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508561 511872 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 507127 508557 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 505247 507130 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00013 42325 46224 EF0149 0/0 99.5 94.3 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00003 55738 56664 efaA 0/0 100.0 99.7 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00007 116938 122901 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 504309 505153 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948879
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00006 150491 152515 ace 0/0 100 96.9 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00004 101375 102385 bopD 0/0 100 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00002 99283 100098 cpsA 0/0 100 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00002 98486 99286 cpsB 0/0 100 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 162063 165374 ebpA 0/0 100 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 160629 162059 ebpB 0/0 100 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 158749 160632 ebpC 1/6 100 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00003 16103 19117 EF0818 0/0 100 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00005 42479 46597 EF3023 0/0 100 98.5 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00001 557717 558643 efaA 0/0 100 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 421437 422168 fsrA 0/0 100 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 420620 421348 fsrB 0/0 100 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 419280 420623 fsrC 0/0 100 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00007 2843 8806 fss1 0/0 100 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 417513 419045 gelE 0/0 100 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 416610 417464 sprE 0/0 100 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00006 157801 158655 srtC 0/0 100 99.2 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948880
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00002 61061 62071 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00006 191502 192317 cpsA 0/0 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 190705 191505 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 189063 190232 cpsC 0/0 100.0 99.4 NP_816139 (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 187578 189044 cpsD 0/0 100.0 98.8 NP_816138 (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 184998 187508 cpsE 0/0 100.0 99.2 NP_816137 (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 184123 184974 cpsF 0/0 100.0 99.9 NP_816136 (cpsF) CpsF protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 181643 184096 cpsG 0/0 100.0 99.4 NP_816135 (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 181227 181625 cpsH 0/0 100.0 99.8 NP_816134 (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 180029 181168 cpsI 0/0 100.0 100.0 NP_816133 (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 178660 180003 cpsJ 0/0 100.0 100.0 NP_816132 (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 177848 178660 cpsK 0/0 100.0 99.0 NP_816131 (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00019 5642 6880 cylA 0/0 100.0 99.4 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 6877 9021 cylB 0/0 100.0 99.7 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 4658 5641 cylI 0/0 100.0 97.2 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12300 12506 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 9033 12014 cylM 0/0 100.0 99.6 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12625 12909 cylR1 0/0 100.0 98.6 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12910 13110 cylR2 0/0 100.0 99.5 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12075 12266 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 33491 36802 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 36806 38236 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 38233 40116 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00014 42325 46224 EF0149 0/0 99.5 94.3 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00003 124750 128612 EF3023 0/0 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00007 56246 57172 efaA 0/0 100.0 99.7 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00008 116938 122901 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 40210 41054 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948881
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00006 147577 149601 ace 0/0 100 97.0 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00003 140001 141011 bopD 0/0 100 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00011 20269 21084 cpsA 0/0 100 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00011 19472 20272 cpsB 0/0 100 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 159149 162460 ebpA 0/0 100 99.4 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 157715 159145 ebpB 0/0 100 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 155835 157718 ebpC 1/6 100 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00002 16103 19117 EF0818 0/0 100 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00001 476710 477636 efaA 0/0 100 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 311577 312308 fsrA 0/0 100 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 310760 311488 fsrB 0/0 100 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 309420 310763 fsrC 0/0 100 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00004 98319 104282 fss1 0/0 100 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 307653 309185 gelE 0/0 100 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 306750 307604 sprE 0/0 100 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00006 154887 155741 srtC 0/0 100 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948882
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00010 18368 20533 acm 0/0 100.0 100.0 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00020 23250 26421 fss3 0/0 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00048 3922 4896 sgrA 0/0 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
SRR8948883
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00014 49159 51324 acm 0/0 100.0 96.9 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00034 18672 21899 ecbA 0/0 100.0 100.0 ZP_00603098 (ecbA) Collagen binding MSCRAMM EcbA [EcbA (VF0539)] [Enterococcus faecium DO]
contig00003 95655 98826 fss3 0/0 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00042 3783 4757 sgrA 0/0 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
SRR8948884
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00004 150656 152680 ace 0/0 100 97.0 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00001 139741 140751 bopD 0/0 100 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00010 20269 21084 cpsA 0/0 100 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00010 19472 20272 cpsB 0/0 100 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00004 162228 165539 ebpA 0/0 100 99.4 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 160794 162224 ebpB 0/0 100 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 158914 160797 ebpC 1/6 100 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 273341 276355 EF0818 0/0 100 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00002 476710 477636 efaA 0/0 100 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00002 311577 312308 fsrA 0/0 100 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 310760 311488 fsrB 0/0 100 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 309420 310763 fsrC 0/0 100 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00005 5654 11617 fss1 0/0 100 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00002 307653 309185 gelE 0/0 100 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00002 306750 307604 sprE 0/0 100 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00004 157966 158820 srtC 0/0 100 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948885
## [1] "NO VIRULENCE FACTORS DETECTED!!!"
SRR8948886
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00011 80554 82734 acm 1/15 100 96.2 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
SRR8948887
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00005 150491 152515 ace 0/0 100 96.9 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00002 101375 102385 bopD 0/0 100 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00003 99283 100098 cpsA 0/0 100 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 98486 99286 cpsB 0/0 100 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00005 162063 165374 ebpA 0/0 100 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00005 160629 162059 ebpB 0/0 100 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00005 158749 160632 ebpC 1/6 100 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00002 234974 237988 EF0818 0/0 100 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00004 42444 46562 EF3023 0/0 100 98.5 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00001 557717 558643 efaA 0/0 100 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 421437 422168 fsrA 0/0 100 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 420620 421348 fsrB 0/0 100 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 419280 420623 fsrC 0/0 100 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00006 2843 8806 fss1 0/0 100 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 417513 419045 gelE 0/0 100 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 416610 417464 sprE 0/0 100 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00005 157801 158655 srtC 0/0 100 99.2 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948888
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00002 123250 124260 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00005 194106 194921 cpsA 0/0 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00005 193309 194109 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00021 7897 9135 cylA 0/0 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 9132 11276 cylB 0/0 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 6913 7896 cylI 0/0 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14555 14761 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 11288 14269 cylM 0/0 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14880 15164 cylR1 0/0 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 15165 15365 cylR2 0/0 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14330 14521 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 182154 186071 EF0149 0/0 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00009 102987 106849 EF3023 0/0 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00011 39052 39978 efaA 0/0 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00004 131651 137614 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 88814 92041 fss3 0/0 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00006 155106 156638 gelE 0/0 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 29749 33666 prgB/asc10 2/4 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00006 154203 155057 sprE 0/0 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948889
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00021 18371 20536 acm 0/0 100.0 100.0 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00005 119923 120933 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00004 194106 194921 cpsA 0/0 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00004 193309 194109 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00088 6895 8133 cylA 0/0 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 8130 10274 cylB 0/0 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 5911 6894 cylI 0/0 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 13553 13759 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 10286 13267 cylM 0/0 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 13878 14162 cylR1 0/0 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 14163 14363 cylR2 0/0 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00088 13328 13519 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508484 511795 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 507050 508480 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 505170 507053 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00003 182144 186061 EF0149 0/0 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00018 25912 29837 EF0485 3/11 100.0 95.3 NP_814266 (EF0485) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00014 61954 65816 EF3023 0/0 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00015 39052 39978 efaA 0/0 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00003 131641 137604 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 88814 92041 fss3 0/0 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00035 24478 27649 fss3 0/0 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00043 22144 23676 gelE 0/0 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00047 23559 27476 prgB/asc10 2/4 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00133 2479 3453 sgrA 0/0 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
contig00043 21241 22095 sprE 0/0 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 504232 505076 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948890
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00002 123102 124112 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00005 194106 194921 cpsA 0/0 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00005 193309 194109 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00024 7897 9135 cylA 0/0 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 9132 11276 cylB 0/0 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 6913 7896 cylI 0/0 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14555 14761 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 11288 14269 cylM 0/0 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14880 15164 cylR1 0/0 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 15165 15365 cylR2 0/0 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14330 14521 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 182154 186071 EF0149 0/0 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00011 39352 40278 efaA 0/0 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00004 131651 137614 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 88814 92041 fss3 0/0 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00014 22144 23676 gelE 0/0 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 30817 34734 prgB/asc10 2/4 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00014 21241 22095 sprE 0/0 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948891
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00002 121590 122600 bopD 0/0 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00006 194106 194921 cpsA 0/0 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 193309 194109 cpsB 0/0 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00020 7897 9135 cylA 0/0 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 9132 11276 cylB 0/0 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 6913 7896 cylI 0/0 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14555 14761 cylL 0/0 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 11288 14269 cylM 0/0 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14880 15164 cylR1 0/0 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 15165 15365 cylR2 0/0 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14330 14521 cylS 0/0 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 ebpA 0/0 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 ebpB 0/0 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 ebpC 1/6 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 182154 186071 EF0149 0/0 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00009 102987 106849 EF3023 0/0 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00011 39052 39978 efaA 0/0 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00004 131651 137614 fss1 0/0 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 88814 92041 fss3 0/0 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00007 155106 156638 gelE 0/0 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 29918 33835 prgB/asc10 2/4 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00007 154203 155057 sprE 0/0 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 srtC 0/0 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]


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Multi-Locus Sequence Typing (MLST)


Symbol Meaning
~ novel full length allele similar to match
? partial match to known allele
- allele missing


Scheme ST 1 2 3 4 5 6 7
SRR8948878 efaecalis 16 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(7) yqiL(6)
SRR8948879 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948880 efaecalis 16 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(7) yqiL(6)
SRR8948881 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948882 efaecium 80 atpA(9) ddl(1) gdh(1) purK(1) gyd(12) pstS(1) adk(1)
SRR8948883 efaecium 203 atpA(15) ddl(1) gdh(1) purK(1) gyd(1) pstS(20) adk(1)
SRR8948884 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948885 - -
SRR8948886 efaecium 1446 atpA(11) ddl(13) gdh(18) purK(15) gyd(10) pstS(19) adk(6)
SRR8948887 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948888 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948889 efaecalis - gdh(5,92) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948890 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948891 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)

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Pangenome Analysis

Pangenome genes summary

Genes Description Number
Core genes (99% <= strains <= 100%) 0
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 5574
Cloud genes (0% <= strains < 15%) 5418
Total genes (0% <= strains <= 100%) 10992

Schematic representation of genes presence (color) or absence (blank) between samples:


Pangenome tree based on presence/absence of accesory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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